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Functions getAsMap and getNegLog10GQ now handle missing genotype case.

This commit is contained in:
Laurent Francioli 2011-11-03 13:04:11 +01:00
parent 19ad5b635a
commit 893787de53
1 changed files with 6 additions and 0 deletions
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6
public/java/src/org/broadinstitute/sting/utils/variantcontext/GenotypeLikelihoods.java
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@ -101,9 +101,12 @@ public class GenotypeLikelihoods {
} }
//Return genotype likelihoods as an EnumMap with Genotypes as keys and likelihoods as values //Return genotype likelihoods as an EnumMap with Genotypes as keys and likelihoods as values
//Returns null in case of missing likelihoods
public EnumMap<Genotype.Type,Double> getAsMap(boolean normalizeFromLog10){ public EnumMap<Genotype.Type,Double> getAsMap(boolean normalizeFromLog10){
//Make sure that the log10likelihoods are set //Make sure that the log10likelihoods are set
double[] likelihoods = normalizeFromLog10 ? MathUtils.normalizeFromLog10(getAsVector()) : getAsVector(); double[] likelihoods = normalizeFromLog10 ? MathUtils.normalizeFromLog10(getAsVector()) : getAsVector();
if(likelihoods == null)
return null;
EnumMap<Genotype.Type,Double> likelihoodsMap = new EnumMap<Genotype.Type, Double>(Genotype.Type.class); EnumMap<Genotype.Type,Double> likelihoodsMap = new EnumMap<Genotype.Type, Double>(Genotype.Type.class);
likelihoodsMap.put(Genotype.Type.HOM_REF,likelihoods[Genotype.Type.HOM_REF.ordinal()-1]); likelihoodsMap.put(Genotype.Type.HOM_REF,likelihoods[Genotype.Type.HOM_REF.ordinal()-1]);
likelihoodsMap.put(Genotype.Type.HET,likelihoods[Genotype.Type.HET.ordinal()-1]); likelihoodsMap.put(Genotype.Type.HET,likelihoods[Genotype.Type.HET.ordinal()-1]);
@ -112,10 +115,13 @@ public class GenotypeLikelihoods {
} }
//Return the neg log10 Genotype Quality (GQ) for the given genotype //Return the neg log10 Genotype Quality (GQ) for the given genotype
//Returns Double.NEGATIVE_INFINITY in case of missing genotype
public double getNegLog10GQ(Genotype.Type genotype){ public double getNegLog10GQ(Genotype.Type genotype){
double qual = Double.NEGATIVE_INFINITY; double qual = Double.NEGATIVE_INFINITY;
EnumMap<Genotype.Type,Double> likelihoods = getAsMap(false); EnumMap<Genotype.Type,Double> likelihoods = getAsMap(false);
if(likelihoods == null)
return qual;
for(Map.Entry<Genotype.Type,Double> likelihood : likelihoods.entrySet()){ for(Map.Entry<Genotype.Type,Double> likelihood : likelihoods.entrySet()){
if(likelihood.getKey() == genotype) if(likelihood.getKey() == genotype)
continue; continue;